Heatmap
Raf
Volcano Plot of Significant Genes
Volcano Plot of All Expressed Genes
Enrichments with EnrichR
Upregulated in Mutant
## Uploading data to Enrichr... Done.
## Querying GO_Biological_Process_2018... Done.
## Querying KEGG_2019... Done.
## Parsing results... Done.
Downregulated in Mutant
## Uploading data to Enrichr... Done.
## Querying GO_Biological_Process_2018... Done.
## Querying KEGG_2019... Done.
## Parsing results... Done.
Pathway Visualisation
Toll Signalling Pathway
MAPK Signalling Pathway
Dorsal Target Genes
Dorsal Targets in the Mesoderm
Hypergeometric Test
q = nrow(zscores_meso)
m = nrow(zscores_meso)
n = nrow(counts(dds)) - nrow(zscores_meso)
k = nrow(ue)
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 0
Dorsal Targets in the Neuroectoderm
Hypergeometric Test
q = nrow(zscores_neuroecto)
m = nrow(zscores_neuroecto)
n = nrow(counts(dds)) - nrow(ue)
k = nrow(ue)
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 0
Dorsal Targets in the Ectoderm
Hypergeometric Test
q = nrow(zscores_ecto) - 1
m = nrow(zscores_ecto)
n = nrow(counts(dds)) - nrow(oe)
k = nrow(oe)
phyper(q, m, n, k, lower.tail = FALSE)
## [1] 4.643589e-05
Combined Heatmap
Session Info
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid parallel stats4 stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] png_0.1-7 VennDiagram_1.6.20
## [3] futile.logger_1.4.3 enrichR_3.0
## [5] pathview_1.32.0 org.Dm.eg.db_3.13.0
## [7] msigdbr_7.4.1 ggrepel_0.9.1
## [9] cowplot_1.1.1 ggpubr_0.4.0
## [11] data.table_1.14.0 DT_0.19
## [13] forcats_0.5.1 dplyr_1.0.7
## [15] purrr_0.3.4 readr_2.0.1
## [17] tidyr_1.1.3 tibble_3.1.4
## [19] ggplot2_3.3.5 tidyverse_1.3.1
## [21] stringr_1.4.0 clusterProfiler_4.0.5
## [23] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.60.0
## [25] rtracklayer_1.52.1 Biostrings_2.60.2
## [27] XVector_0.32.0 pheatmap_1.0.12
## [29] geneplotter_1.70.0 annotate_1.70.0
## [31] XML_3.99-0.7 reshape_0.8.8
## [33] lattice_0.20-44 gridExtra_2.3
## [35] RColorBrewer_1.1-2 GenomicFeatures_1.44.2
## [37] AnnotationDbi_1.54.1 knitr_1.33
## [39] DESeq2_1.32.0 SummarizedExperiment_1.22.0
## [41] Biobase_2.52.0 MatrixGenerics_1.4.3
## [43] matrixStats_0.60.1 GenomicRanges_1.44.0
## [45] GenomeInfoDb_1.28.4 IRanges_2.26.0
## [47] S4Vectors_0.30.0 BiocGenerics_0.38.0
##
## loaded via a namespace (and not attached):
## [1] utf8_1.2.2 tidyselect_1.1.1 RSQLite_2.2.8
## [4] htmlwidgets_1.5.4 BiocParallel_1.26.2 scatterpie_0.1.7
## [7] munsell_0.5.0 withr_2.4.2 colorspace_2.0-2
## [10] GOSemSim_2.18.1 filelock_1.0.2 highr_0.9
## [13] rstudioapi_0.13 ggsignif_0.6.2 DOSE_3.18.2
## [16] labeling_0.4.2 KEGGgraph_1.52.0 GenomeInfoDbData_1.2.6
## [19] polyclip_1.10-0 bit64_4.0.5 farver_2.1.0
## [22] rprojroot_2.0.2 downloader_0.4 vctrs_0.3.8
## [25] treeio_1.16.2 generics_0.1.0 lambda.r_1.2.4
## [28] xfun_0.25 BiocFileCache_2.0.0 R6_2.5.1
## [31] graphlayouts_0.7.1 locfit_1.5-9.4 bitops_1.0-7
## [34] cachem_1.0.6 fgsea_1.18.0 gridGraphics_0.5-1
## [37] DelayedArray_0.18.0 assertthat_0.2.1 BiocIO_1.2.0
## [40] scales_1.1.1 ggraph_2.0.5 enrichplot_1.12.2
## [43] gtable_0.3.0 tidygraph_1.2.0 rlang_0.4.11
## [46] genefilter_1.74.0 splines_4.1.1 rstatix_0.7.0
## [49] lazyeval_0.2.2 broom_0.7.9 abind_1.4-5
## [52] yaml_2.2.1 reshape2_1.4.4 modelr_0.1.8
## [55] crosstalk_1.1.1 backports_1.2.1 qvalue_2.24.0
## [58] tools_4.1.1 ggplotify_0.1.0 ellipsis_0.3.2
## [61] jquerylib_0.1.4 Rcpp_1.0.7 plyr_1.8.6
## [64] progress_1.2.2 zlibbioc_1.38.0 RCurl_1.98-1.4
## [67] prettyunits_1.1.1 viridis_0.6.1 haven_2.4.3
## [70] fs_1.5.0 magrittr_2.0.1 futile.options_1.0.1
## [73] DO.db_2.9 openxlsx_4.2.4 reprex_2.0.1
## [76] hms_1.1.0 patchwork_1.1.1 evaluate_0.14
## [79] xtable_1.8-4 rio_0.5.27 readxl_1.3.1
## [82] compiler_4.1.1 biomaRt_2.48.3 crayon_1.4.1
## [85] shadowtext_0.0.9 htmltools_0.5.2 ggfun_0.0.4
## [88] tzdb_0.1.2 aplot_0.1.1 lubridate_1.7.10
## [91] DBI_1.1.1 formatR_1.11 tweenr_1.0.2
## [94] dbplyr_2.1.1 MASS_7.3-54 rappdirs_0.3.3
## [97] babelgene_21.4 Matrix_1.3-4 car_3.0-11
## [100] cli_3.0.1 igraph_1.2.6 pkgconfig_2.0.3
## [103] GenomicAlignments_1.28.0 foreign_0.8-81 xml2_1.3.2
## [106] ggtree_3.0.4 rvest_1.0.1 yulab.utils_0.0.2
## [109] digest_0.6.27 graph_1.70.0 rmarkdown_2.10
## [112] cellranger_1.1.0 fastmatch_1.1-3 tidytree_0.3.5
## [115] restfulr_0.0.13 curl_4.3.2 Rsamtools_2.8.0
## [118] rjson_0.2.20 lifecycle_1.0.0 nlme_3.1-152
## [121] jsonlite_1.7.2 carData_3.0-4 viridisLite_0.4.0
## [124] fansi_0.5.0 pillar_1.6.2 KEGGREST_1.32.0
## [127] fastmap_1.1.0 httr_1.4.2 survival_3.2-11
## [130] GO.db_3.13.0 glue_1.4.2 zip_2.2.0
## [133] Rgraphviz_2.36.0 bit_4.0.4 ggforce_0.3.3
## [136] stringi_1.7.4 blob_1.2.2 org.Hs.eg.db_3.13.0
## [139] memoise_2.0.0 ape_5.5